Thursday, June 28, 2012

This Paper Will Be Cited As Showing How Those Complex Ion Channels Evolved

If you thought that Harold Zakon’s blunder in the very first sentence of his new PNAS paper, on the evolution of voltage-gated sodium channels, was merely the obligatory secret handshake and that thereafter Zakon would get down to business with some real science, well, think again. After his rather shaky start you’ll find that the second sentence is even worse than the first:

The nervous system and muscles evolved shortly thereafter.

Zakon gives no citation on this claim. Apparently it is one of evolution’s brute facts which evolutionists need merely to remind themselves of occasionally.

Later Zakon does admit to some problems with the evolutionary tree:

The phylogeny of basal metazoans is poorly resolved, likely because of the rapid radiation of these then-new life forms

So not only did metazoans just happen to arise spontaneously, but they did so in a “rapid radiation.” For every failure of evolutionary theory you can bet there are always the usual explanatory devices competing to fill the gap.

Not bad for something from nothing. As you can see, that just has random mutations written all over it. After all, such molecular engineering marvels just “appear” at some long lost unobservable time and place:

Potassium leak and voltage-dependent K+ (Kv) channels appeared three billion years ago in bacteria and occur in all organisms

Potassium channels “appeared” three billion years ago? For this claim Zakon cites a paper written by evolutionists who presuppose that potassium channels (and everything else for that matter) evolved. In other words, to support his unscientific assertion that potassium channels “appeared” three billion years ago, Zakon cites the work of evolutionists who assume that potassium channels “appeared” at some point.

Just when you thought this evolutionary tale could not become any more bizarre, Zakon explains how he believes these potassium channels “appeared”:

Kv channels are the “founding members” of the family of ion-permeating channels whose basic structure is a protein of six transmembrane helices (6TM) that associate as tetramers to form a channel. At some point early in eukaryote evolution, the gene for a 6TM channel likely duplicated, giving rise to a protein with two domains. These proteins then dimerized to form a complete channel. Such a channel still exists in the two-pore channel family of Ca2+-permeable channels localized in endosomes and lysozomes. The gene for a two domain channel likely duplicated to make a protein with four domains capable of forming a channel on its own (4x6TM). Eventually such a four-domain channel evolved (or retained) permeability to Ca2+, and these handily became involved in intracellular signaling. Other Ca2+-binding proteins and enzymes first appeared in single-celled eukaryotes. Additionally, there are single 6TM Na+-permeable channels in bacteria. Their relationship to eukaryotic [sodium] channels is unclear, and they will not be discussed in this review.

In the world of an evolutionists, astronomically complex structures just happen to form spontaneously. Things appear, duplicate, modify, retain, evolve, serendipitously perform new functions, and so forth.

Zakon goes on to explain that calcium channels also “appear early in animals.” Furthermore, it has been confirmed that sodium channels evolved from calcium channels. And how could evolutionists make such an astonishing discovery? Easy, by comparing the structures and amino acid sequences of these marvels, such as in choanoflagellates:

Analysis of putative Cav and Nav channel genes from fungi, choanoflagellates, and metazoans confirm this speculation and show that choanoflagellates have a channel that groups with recognized [sodium] channels with strong support.

Though they cannot explain how even a single protein could evolve, evolutionists conclude that voltage-gated sodium channels evolved from calcium channels because they share certain similarities.

Later we learn that a variety of key molecular components were luckily finally in place “for construction of the nodes of Ranvier.”

And that electric organs evolved independently in African and American fish as the sodium channel gene “underwent a burst of evolutionary change at the origin of both groups of electric fishes, with numerous substitutions in key regions of the channel.”

Then there are the various neurotoxins, such as tetrodotoxin, that interfere with the sodium channel. Vertebrates that maintain high concentrations of tetrodotoxin must somehow protect their several types of sodium channels from the dangerous poison.

For example, hundreds of fish species, such as the Pufferfish, safely maintain high concentrations of tetrodotoxin with sodium channel genes that have slight differences which help to make the fish immune to tetrodotoxin. But how could these similar differences have evolved in all these different fish species? The slow process of random mutations would require too much time to save a species from its internal poison. Furthermore these modifications would be required in not just one, but all the different sodium channel genes. Once again evolution has an explanatory device:

We still do not know how pufferfish were able to survive with only one or a few tetrodotoxin-resistant [sodium] channels. The most likely scenario is that tetrodotoxin-resistant mutations accumulated gradually in the [sodium] channel genes as fish were initially exposed to a light load of tetrodotoxin. Gradually, as more channels gained resistance, they were able to carry a greater toxic load.

There is always a just-so story.

Then there are the garter snakes and their prey, the newts. Newts maintain high concentrations of tetrodotoxin and garter snakes that eat them have sodium channel genes with the right, immunizing, modifications.

But garter snakes that live in different areas do not have these modifications, and may die if they ingest a newt. In fact it appears that the different garter snakes populations that prey on newts would have had to independently evolve their sodium channel modifications:

Even more striking, tetrodotoxin resistance has evolved multiple times in populations of other species of garter snakes that are also sympatric with newts in the Pacific Northwest and California, as well as other snake species sympatric with other newts or frogs that use tetrodotoxin in South America and Asia.

But that’s not all. The newt larvae do not produce the tetrodotoxin poison but since the adult newts can be cannibalistic the larvae will flee when they smell tetrodotoxin nearby. So in this case tetrodotoxin is a chemical signal. This is also true in pufferfish when males detect nanomolar levels of tetrodotoxin resulting from female egg laying.

This is all fascinating biology and ion channels, such as these voltage-gated sodium channels, are incredible molecular machines. And while it is true that all of this can be explained in a speculative evolutionary narrative, the story here is that, as usual, the biology does not easily fit evolutionary theory. Papers such as this one are cited as yet more confirmations of evolutionary theory, but in fact they are little more than evolutionary story-telling.

39 comments:

Off Topic: Dr. Hunter, I don't know if you've seen this article yet, but I think you will find it very interesting:

Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson)Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says.Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885

It may not be what evolutionists nor atheists think but it's certainly what Mr. Zakon means when he claims things "appeared" and "likely duplicated". If not he'd have provided something other than those terms.

He is doing good science. He's asking Mr. Zakon and others at least this:

1.How potassium leak and voltage-dependent K+ (Kv) channels and Ca2+-binding proteins and enzymes simply appeared and

Did you even bother looking at the paper? References to other scientific investigations on the development of K+ channels and Ca2+ proteins are provided.

2. How certain genes "likely duplicated".

Gene duplication is an extremely common and well documented empirically observed phenomenon. Zakon is offering a hypothesis (not specifically addressed by his paper) that gene duplication is a plausible candidate for the multi-domain proteins.

Zakon assumes the truth of those statements. But assuming the truth of something isn't good science, right?

When the assumptions are based on sound reasoning and available evidence as in this case, it's a perfectly valid method of doing good science.

1. Mr. Zakon referenced only one paper on the development of K+ channels and Ca2 proteins as far as I could tell (citation 11). It's the one Mr. Hunter notes. What are the others? And, again, as far as I can tell from the abstract, the authors of that paper seem to assume that these arose after "millions of years of evolution".

2. I'm a novice so forgive the questions: how does one demonstrate that gene duplication occurred then? And how does one explain the rise of gene duplication at all, all those years ago?

I see your point on sound reasoning and available evidence. I also see the point of asking whether it's sound reason build around a series of unproven and perhaps unprovable assumptions. Either way, it's also good science to ask whether sound reasoning is occurring.

1. Mr. Zakon referenced only one paper on the development of K+ channels and Ca2 proteins as far as I could tell (citation 11). It's the one Mr. Hunter notes. What are the others?

And reference 12. And reference 13. And reference 14. And reference 15.

Try actually reading the paper. Jeeze.

And, again, as far as I can tell from the abstract, the authors of that paper seem to assume that these arose after "millions of years of evolution".

Why shouldn't they? That is an extremely well supported and valid assumption.

2. I'm a novice so forgive the questions: how does one demonstrate that gene duplication occurred then?

By empirically observing either the event or the evidence the event leaves. Google Scholar lists over 300,000 references on the topic.

And how does one explain the rise of gene duplication at all, all those years ago?

It seems to be an inherent property of the self-sustaining chemical reactions used by imperfect replicators. Asking why the laws of chemistry and physics are the way they are is way beyond the scope of this discussion.

I see your point on sound reasoning and available evidence. I also see the point of asking whether it's sound reason build around a series of unproven and perhaps unprovable assumptions.

Asking is fine. You were answered and provided with reasons why the technical assumptions made were justified. But if you want to understand the gory details better you're going to have to do some research yourself. The information is readily available.

Either way, it's also good science to ask whether sound reasoning is occurring.

Agreed. Real scientists question each other that way all the time. You are certainly free to provide any evidence that unsound reasoning is occurring or that or bad assumptions are being made. But merely asserting such things without support as CH is wont to do just doesn't cut it.

NOW this is the next tale, and it tells how Cornelius got his big Harrumph.

In the beginning of years, when the world was so new and all, there was Cornelius, and he lived in the middle of a Howling Desert because he did not want to do science; and besides, he was a Howler himself. So he wrote blogs and books and polemics, most 'scruciating idle; and when anybody spoke to him he said 'Harrumph!' Just 'Harrumph!' and no more.

Presently the Physicist came to him on Monday morning, with an equation in his hand, and said ‘Cornelius, O Cornelius, come out and test some hypotheses like the rest of us.'

'Harrumph!' said Cornelius; and the Physicist went away.

Presently the Biologist came to him, with a bacterial culture in his hand, said, ‘Cornelius, O Cornelius, come and test some hypotheses with the rest of us.'

'Harrumph!' said Cornelius; and the Biologist went away.

Presently the Statistician came to him, with a spreadsheet in his hand and said, ‘Cornelius, O Cornelius, come and test some hypotheses like the rest of us.'

'Harrumph!' said Cornelius; and the Statistician went away.

Presently there came along the Djinn in charge of All Deserts, rolling in a cloud of dust (Djinns always travel that way because it is Magic), and he stopped to palaver and pow-pow with the scientists.

'Djinn of All Deserts,' said the Physicist, 'is it right for any one to be idle, with the world so new-and-all, and so much to find out about it?'

'Certainly not,' said the Djinn.

'Well,' said the Physicist, 'there's a thing in the middle of your Howling Desert (and he's a Howler himself) and he hasn't done a stroke of science since Monday morning.'

'Whew!' said the Djinn, whistling, 'that's my Cornelius, for all the gold in Arabia! What does he say about it?'

'He says "'Harrumph!"' said the Biologist; 'and he won't collect any data.'

'Does he say anything else?'

'Only "'Harrumph!"; and he won't do any data analysis,' said the Statistician.

'Very good,' said the Djinn. 'I'll harrumph him if you will kindly wait a minute.'

The Djinn rolled himself up in his dust-cloak, and took a bearing across the desert, and found Cornelius most 'scruciatingly idle, looking at his own reflection in a pool of water.

'My long and bubbling friend,' said the Djinn, 'what's this I hear of your doing no science, with the world so new-and-all?'

'Harrumph!' said Cornelius.

The Djinn sat down, with his chin in his hand, and began to think a Great Magic, while Cornelius looked at his own reflection in the pool of water.

'You've given the Scientists extra work ever since Monday morning, all on account of your 'scruciating idleness,' said the Djinn; and he went on thinking Magics, with his chin in his hand.

'Harrumph!' said the Camel.

'I shouldn't say that again if I were you,' said the Djinn; 'you might say it once too often. Bubbles, I want you to write about science.'

And Cornelius said 'Harrumph!' again; but no sooner had he said it than he saw his writing, that he was so proud of, puffing up and puffing up into a great big lolloping Harrumph.

'Do you see that?' said the Djinn. 'That's your very own Harrumph that you've brought upon your very own self by not doing science. Now you are going to work.'

And from that day to this Cornelius always writes a 'Harrumph (we call it ‘blog’ now, not to hurt his feelings); but he has never yet learned how to test a hypothesis.

Pedant said: "If he were serious, he'd contact Zakon and report the answer back to us."

And if Harold Zakon was so confident in his research, he'd do a simple search for criticism and attempt to address it. Google brings up this thread as the 4rth result for "Harold Zakon’s".

Right. I'm sure a working scientist has nothing better to do all day than scour the web for baseless criticisms from wackaloon Creationist blogs.

Here's an idea: Why don't you write up your detailed criticisms and present them to him, or to PNAS? You'd stand a much better chance of getting them addressed than just hiding in the bushes and throwing rocks.

And Elizabeth, what do you believe if not that living things and their components and their predecessors 'formed spontaneously?' Your objection gives you only two words on which to equivocate - "form" and "spontaneously." To which do you object, and on what grounds?

"Spontaneous" couldn't be a more fitting word, as its only specification is what it excludes. To say that any part of OOL or evolution was not spontaneous is to say that it results from either purpose or natural law, literally by definition.

And Elizabeth, what do you believe if not that living things and their components and their predecessors 'formed spontaneously?' Your objection gives you only two words on which to equivocate - "form" and "spontaneously." To which do you object, and on what grounds?

Both, because the full sentence was: "astronomically complex structures just happen to form spontaneously."

No, they don't "just happen to form spontaneously" - they start simple, by a very specific set of mechanisms, gradually become more complex.

"Spontaneous" couldn't be a more fitting word, as its only specification is what it excludes. To say that any part of OOL or evolution was not spontaneous is to say that it results from either purpose or natural law, literally by definition.

Well if by "spontaneous" you mean "not by natural law" that's a very odd use of the word. I do think living organisms evolved and function according to "natural law" - but that isn't why I object to the parody claim, which seemed to me to imply that "evolutionists" imagine that "astronomically complex structures" "just happen" to come into being from ex nihilo.

If Cornelius meant that we think that "astronomically complex structures" are the result of the working out of natural laws intrinsic to the universe, then fine. But then, weirdly, according to your definition of "spontaneous", that wouldn't be "spontaneous"!

Either way, Cornelius' phrase does not capture what any "evolutionist" I know actually thinks. It's yet another of Cornelius's straw men.

"My objection to ID isn't that I think it's false, but that I think that the inference of an ID from the evidence is fallacious."

I´m not an ID supporter because I think is impossible to prove design scientifically. But to be honest in my old Lehninger the best hypotesis for OOL were alliens seeding the life on earth and nobody call that hypotesis "fallacious" looking very similar to me.And to put all in perspective I also think that ToE and OOL are also impossible to be scientifically demostrates.

You have responded not to "spontaneous," which I did not use in an odd way. I used it exactly according to its precise definition. Purpose and natural law are exactly what it rules out.

You have responded to "instantaneous," except that no one used that word. No one thinks that, and no one thinks you think that.

For a thing to happen over billions of years doesn't make it any less spontaneous than appearing in moment. There are no natural laws that cause such things to happen. There is only the vague, unfounded assumption that varying self-replicators somehow form a "law" of their own. Then to support this undefined "law," another is needed to explain the existence of such varying self-replicators.

"If Cornelius meant that we think that "astronomically complex structures" are the result of the working out of natural laws intrinsic to the universe, then fine. But then, weirdly, according to your definition of "spontaneous", that wouldn't be "spontaneous"!"

You would be fine with Cornelious attributing that to you? Why? To what 'natural laws intrinsic to the universe' to you refer? There's not an ounce of consensus on how evolution or OOL occurred. If one person believes in God because of the "final" results and another believes unspecified, undiscovered natural laws which must exist, what is the difference? Neither are science.

And that's not a "weird" use of "spontaneous." It's straight out of any dictionary without having to dig for it.

What an amazingly ignorant thing to claim. There is an overwhelming scientific consensus on how evolution has occurred. You can take classes about it at most every college or university. You can learn about it at any natural history museum, or from any number of good science books and web sites. You can read about the details in literally millions of peer reviewed scientific articles.

I'll never understand why Creationists think that if they make ridiculous claims and deny the evidence, the evidence somehow magically goes away.

BTW Scott,you still haven't provided your *alternate* explanation for the last 650 MY of the fossil record. Are you just too ashamed to admit you don't have one?

badwiring:"If Cornelius meant that we think that "astronomically complex structures" are the result of the working out of natural laws intrinsic to the universe, then fine. But then, weirdly, according to your definition of "spontaneous", that wouldn't be "spontaneous"!"

You would be fine with Cornelious attributing that to you?

Yes.

Why? To what 'natural laws intrinsic to the universe' to you refer?

Well, a "natural law" is a principle that scientist have formulated that seems to work, and there are many phenomena that we have not yet formulated a "natural law" for. But the principle of scientific methodology is that the universe is predictable, and that the laws that govern it are discoverable. So first of all my practical assumption is that what we observe is the result of the working out of the natural laws (whether discovered or undiscovered) of the universe, and secondly, I see no good reason to think that there exist phenomena that are not discoverable by natural laws. That wouldn't in it itself make me an atheist though. I don't see why a creator deity couldn't figure out how to set up a universe with laws that meant that it did what this one did.

There's not an ounce of consensus on how evolution or OOL occurred.

Oh, there are a few ounces, but there are certainly competing models. That's how science is done.

If one person believes in God because of the "final" results and another believes unspecified, undiscovered natural laws which must exist, what is the difference? Neither are science.

Well, the first isn't, but the second can be either a working methodological assumption (the one on which scientific methodology is based, and which is sometimes called "methodological naturalism") or a philosophical position (sometimes called "philosophical naturalism". As I scientist I must adopt the first, but that has no relevance to whether or not I also adopt the second. You can be a scientist and believe in miracles. It's just that science does not have the tools to detect miracles.